‘Bioinformatics for geneticists and biologists (BIGB02)

Delivered by Dr. Nic Blouin and Dr Ian Misner

http://www.prstatistics.com/course/bioinformatics-for-geneticists-and-biologists-bigb02/

This course will run from 3rd – 7th July 2017 at SCENE Field Station, Loch Lomond, Glasgow

OVERVIEW
The handling of large datasets has become intractable without some level of bioinformatic literacy. Many biologists find that there is a steep learning curve to develop the confidence required to explore their genomics datasets effectively. This bioinformatics short course includes a rich collection of hands-on instruction and lectures specifically intended to help novice users become comfortable with a range of tools currently used to analyse next-generation data.

INTENDED AUDIENCE
The course is aimed at anyone interested in learning bioinformatics tools needed for handling large genomic datasets.

Course content is as follows

Monday 3rd – Classes from 09:00 to 17:00
Module 1: Linux.
Linux is taught on the first day, this takes the entire day. Once you get through this portion you will be on your way to completing your own NGS analysis. We have created a workbook for this portion of the course. This is a step-by-step, or in the case, command-by-command, Linux guide. We complete each command as a class and discuss and review issues along the way.

Tuesday 4th – Classes from 09:00 to 17:00
Module 2: RNAseq.
We will cover two of the more popular tools in this workshop, The Tuxedo package & Trinity. Outcomes; Confidence to design effective RNAseq experiments. Knowledge of NGS sequencing platforms and their differing applications, ability to analyze Illumina data for quality and contamination. Proficiency to implement the Tuxedo package to analyze an RNAseq dataset.Create publication ready graphics with cummeRbund and EdgeR.

Wednesday 5th – Classes from 09:00 to 17:00
Module 3: Assembly.
Whether you have a reference genome or are working with de novo samples there are some basic tools and practices that we cover to help assist you in your genome project. In this module we will cover the basic metrics you should review when doing assembly as well as best practices to consider in your own project. Outcomes; Take raw reads through a complete assembly process. Working knowledge of different assembly issues/challenges. The effect of assembly settings on assembly outcomes.

Thursday 6th – Classes from 09:00 to 17:00
Module 4: Annotation.
We will use MAKER and Blast2GO and annotate the genome we assembled in the assembly module. Outcomes; Understand the differences between functional and structural annotations. Train MAKER to improve structural annotations. Understand how MAKER improves with more evidence and training; visualize structural annotations. Apply functional annotations with Blast2GO.

Friday 7th – Classes from 09:00 to 16:00
Module 5: Python.
Why Python? In truth it doesn’t matter what coding language you learn but you should learn one. Python has a very straightforward syntax that is easy to understand.In this module we will utilise the clearly explained training examples from Python for Biologists. Outcomes; Understand Python language syntax. Create scripts to answer biological problems & parse and analyse BLAST outputs using custom Python code.

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Upcoming courses - email for details [log in to unmask]

1.	ADVANCES IN MULTIVARIATE ANALYSIS OF SPATIAL ECOLOGICAL DATA USING R #MVSP
3rd – 7th April 2017, Scotland, Prof. Pierre Legendre, Dr. Olivier Gauthier
http://www.prstatistics.com/course/advances-in-spatial-analysis-of-multivariate-ecological-data-theory-and-practice-mvsp02/

2.	ADVANCING IN STATISTICAL MODELLING FOR EVOLUTIONARY BIOLOGISTS AND ECOLOGISTS USING R #ADVR
17th – 21st April 2017, Scotland, Dr. Luc Bussiere, Dr. Ane Timenes Laugen
http://www.prstatistics.com/course/advancing-statistical-modelling-using-r-advr06/

3.	CODING, DATA MANAGEMENT AND SHINY APPLICATIONS USING RSTUDIO FOR EVOLUTIONARY BIOLOGISTS AND ECOLOGISTS #CDSR
15th - 19th May, Scotland Dr. Aline Quadros
http://www.prstatistics.com/course/coding-data-management-and-shiny-applications-using-rstudio-for-evolutionary-biologists-and-ecologists-cdsr01/

4.	GEOMETRIC MORPHOMETRICS USING R #GMMR
5th – 9th June 2017, Scotland, Prof. Dean Adams, Prof. Michael Collyer, Dr. Antigoni Kaliontzopoulou
http://www.prstatistics.com/course/geometric-morphometrics-using-r-gmmr01/

5.	MULTIVARIATE ANALYSIS OF SPATIAL ECOLOGICAL DATA #MASE
19th – 23rd June, Canada, Prof. Subhash Lele, Dr. Peter Solymos
http://www.prstatistics.com/course/multivariate-analysis-of-spatial-ecological-data-using-r-mase01/

6.	TIME SERIES MODELS FOR ECOLOGISTS USING R (JUNE 2017 #TSME
26th – 30th June, Canada, Dr. Andrew Parnell
http://www.prstatistics.com/course/time-series-models-foe-ecologists-tsme01/

7.	BIOINFORMATICS FOR GENETICISTS AND BIOLOGISTS #BIGB
3rd – 7th July 2017, Scotland, Dr. Nic Blouin, Dr. Ian Misner
http://www.prstatistics.com/course/bioinformatics-for-geneticists-and-biologists-bigb02/

8.	META-ANALYSIS IN ECOLOGY, EVOLUTION AND ENVIRONMENTAL SCIENCES #METR01
24th – 28th July, Scotland, Prof. Julia Koricheva, Prof. Elena Kulinskaya
http://www.prstatistics.com/course/meta-analysis-in-ecology-evolution-and-environmental-sciences-metr01/

9.	SPATIAL ANALYSIS OF ECOLOGICAL DATA USING R #SPAE
7th – 12th August 2017, Scotland, Prof. Jason Matthiopoulos, Dr. James Grecian
http://www.prstatistics.com/course/spatial-analysis-ecological-data-using-r-spae05/

10.	ECOLOGICAL NICHE MODELLING USING R #ENMR
16th – 20th October 2017, Scotland, Dr. Neftali Sillero
http://www.prstatistics.com/course/ecological-niche-modelling-using-r-enmr01/

11.	INTRODUCTION TO BIOINFORMATICS USING LINUX #IBUL
16th – 20th October, Scotland, Dr. Martin Jones
http://www.prstatistics.com/course/introduction-to-bioinformatics-using-linux-ibul02/

12.	GENETIC DATA ANALYSIS AND EXPLORATION USING R #GDAR
23rd – 27th October, Wales, Dr. Thibaut Jombart, Zhian Kavar
http://www.prstatistics.com/course/genetic-data-analysis-exploration-using-r-gdar03/

13.	STRUCTURAL EQUATION MODELLING FOR ECOLOGISTS AND EVOLUTIONARY BIOLOGISTS USING R #SEMR
23rd – 27th October, Wales, Prof Jarrett Byrnes, Dr. Jon Lefcheck
http://www.prstatistics.com/course/structural-equation-modelling-for-ecologists-and-evolutionary-biologists-semr01/

14.	LANDSCAPE (POPULATION) GENETIC DATA ANALYSIS USING R #LNDG
6th – 10th November, Wales, Prof. Rodney Dyer
http://www.prstatistics.com/course/landscape-genetic-data-analysis-using-r-lndg02/

15.	APPLIED BAYESIAN MODELLING FOR ECOLOGISTS AND EPIDEMIOLOGISTS #ABME
20th - 25th November 2017, Scotland, Prof. Jason Matthiopoulos, Dr. Matt Denwood
http://www.prstatistics.com/course/applied-bayesian-modelling-ecologists-epidemiologists-abme03/

16.	INTRODUCTION REMOTE SENSING AND GIS APPLICATIONS FOR ECOLOGISTS #IRMS
27th Nov – 1st Dec, Wales, Dr Duccio Rocchini, Dr. Luca Delucchi
http://www.prstatistics.com/course/introduction-to-remote-sensing-and-gis-for-ecological-applications-irms01/

17.	INTRODUCTION TO PYTHON FOR BIOLOGISTS #IPYB
27th Nov – 1st Dec, Wales, Dr. Martin Jones
http://www.prstatistics.com/course/introduction-to-python-for-biologists-ipyb04/

18.	DATA VISUALISATION AND MANIPULATION USING PYTHON #DVMP
11th – 15th December 2017, Wales, Dr. Martin Jones
http://www.prstatistics.com/course/data-visualisation-and-manipulation-using-python-dvmp01/

19.	ADVANCING IN STATISTICAL MODELLING USING R #ADVR
11th – 15th December 2017, Wales, Dr. Luc Bussiere, Dr. Tom Houslay, Dr. Ane Timenes Laugen,
http://www.prstatistics.com/course/advancing-statistical-modelling-using-r-advr07/

20.	INTRODUCTION TO BAYESIAN HIERARCHICAL MODELLING #IBHM
29th Jan – 2nd Feb 2018, Scotland, Dr. Andrew Parnell
http://www.prstatistics.com/course/introduction-to-bayesian-hierarchical-modelling-using-r-ibhm02/

21.	ANIMAL MOVEMENT ECOLOGY (February 2018) #ANME
??th - ??th February 2018, Wales, Dr Luca Borger, Dr. John Fieberg

22.	AQUATIC TELEMENTRY DATA ANALYSIS USIR R (TBC) #ATDAR
??th - ??th February 2018, Wales,

23.	FUNCTIONAL ECOLOGY FROM ORGANISM TO ECOSYSTEM: THEORY AND COMPUTATION #FEER
5th – 9th March 2018, Scotland, Dr. Francesco de Bello, Dr. Lars Götzenberger, Dr. Carlos Carmona
http://www.prstatistics.com/course/functional-ecology-from-organism-to-ecosystem-theory-and-computation-feer01/

24.	STABLE ISOTOPE MIXING MODELS USING SIAR, SIBER AND MIXSIAR #SIMM
Dr. Andrew Parnell, Dr. Andrew Jackson – Date and location to be confirmed

25.	NETWORK ANAYLSIS FOR ECOLOGISTS USING R #NTWA
Dr. Marco Scotti - Date and location to be confirmed

26.	MODEL BASE MULTIVARIATE ANALYSIS OF ABUNDANCE DATA USING R #MBMV0
Prof David Warton - Date and location to be confirmed

27.	ADVANCED PYTHON FOR BIOLOGISTS #APYB
Dr. Martin Jones - Date and location to be confirmed

28.	PHYLOGENETIC DATA ANALYSIS USING R (TBC) #PHYL
Dr. Emmanuel Paradis – Date and location to be confirmed


Oliver Hooker PhD.
PR statistics

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-- 
Oliver Hooker PhD.
PR statistics

2017 publications - 
2) Ecosystem size predicts eco-morphological variability in post-glacial diversification. Ecology and Evolution. In press.
1) The physiological costs of prey switching reinforce foraging specialization. Journal of animal ecology.

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